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240 lines
9.4 KiB
Python
240 lines
9.4 KiB
Python
# Copyright 2010 by Thomas Schmitt. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Tests for SeqIO SeqXML module."""
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import unittest
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import sys
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from Bio import SeqIO
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from Bio.Seq import Seq
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from Bio.SeqRecord import SeqRecord
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from io import BytesIO
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def assert_equal_records(testCase, record_a, record_b):
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testCase.assertEqual(record_a.id, record_b.id)
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testCase.assertEqual(record_a.name, record_b.name)
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testCase.assertEqual(record_a.description, record_b.description)
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testCase.assertEqual(str(record_a.seq), str(record_b.seq))
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testCase.assertEqual(record_a.dbxrefs, record_b.dbxrefs)
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testCase.assertEqual(record_a.annotations, record_a.annotations)
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class TestSimpleRead(unittest.TestCase):
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def test_check_SeqIO(self):
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"""Files readable using parser via SeqIO."""
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records = list(SeqIO.parse("SeqXML/dna_example.xml", "seqxml"))
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self.assertEqual(len(records), 4)
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records = list(SeqIO.parse("SeqXML/rna_example.xml", "seqxml"))
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self.assertEqual(len(records), 5)
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records = list(SeqIO.parse("SeqXML/protein_example.xml", "seqxml"))
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self.assertEqual(len(records), 5)
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records = list(SeqIO.parse("SeqXML/global_species_example.xml", "seqxml"))
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self.assertEqual(len(records), 2)
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class TestDetailedRead(unittest.TestCase):
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records = {}
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def setUp(self):
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self.records["dna"] = list(SeqIO.parse("SeqXML/dna_example.xml", "seqxml"))
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self.records["rna"] = list(SeqIO.parse("SeqXML/rna_example.xml", "seqxml"))
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self.records["protein"] = list(
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SeqIO.parse("SeqXML/protein_example.xml", "seqxml")
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)
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self.records["globalSpecies"] = list(
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SeqIO.parse("SeqXML/global_species_example.xml", "seqxml")
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)
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def test_special_characters_desc(self):
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"""Read special XML characters in description."""
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self.assertEqual(
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self.records["dna"][2].description,
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'some special characters in the description\n<tag> "quoted string"',
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)
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def test_unicode_characters_desc(self):
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"""Test special unicode characters in the description."""
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self.assertEqual(self.records["rna"][2].description, "åÅüöÖßø䢣$€香肠")
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def test_full_characters_set_read(self):
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"""Read full characters set for each type."""
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self.assertEqual(str(self.records["dna"][1].seq), "ACGTMRWSYKVHDBXN.-")
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self.assertEqual(str(self.records["rna"][1].seq), "ACGUMRWSYKVHDBXN.-")
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self.assertEqual(
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str(self.records["protein"][1].seq), "ABCDEFGHIJKLMNOPQRSTUVWXYZ.-*"
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)
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def test_duplicated_property(self):
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"""Read property with multiple values."""
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self.assertEqual(
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self.records["protein"][2].annotations["test"], ["1", "2", "3"]
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)
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def test_duplicated_dbxref(self):
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"""Read multiple cross references to a single source."""
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self.assertEqual(
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self.records["protein"][2].dbxrefs, ["someDB:G001", "someDB:G002"]
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)
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def test_read_minimal_required(self):
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"""Check minimal record."""
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minimalRecord = SeqRecord(id="test", seq=Seq("abc"))
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minimalRecord.annotations["source"] = "Ensembl"
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minimalRecord.annotations["molecule_type"] = "DNA"
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self.assertEqual(self.records["rna"][3].name, minimalRecord.name)
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self.assertEqual(self.records["dna"][3].annotations, minimalRecord.annotations)
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self.assertEqual(self.records["rna"][3].dbxrefs, minimalRecord.dbxrefs)
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self.assertEqual(
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self.records["protein"][3].description, minimalRecord.description
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)
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def test_local_species(self):
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"""Check local species."""
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self.assertEqual(self.records["rna"][1].annotations["organism"], "Mus musculus")
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self.assertEqual(self.records["rna"][1].annotations["ncbi_taxid"], "10090")
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self.assertEqual(
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self.records["rna"][0].annotations["organism"], "Gallus gallus"
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)
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self.assertEqual(self.records["rna"][0].annotations["ncbi_taxid"], "9031")
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def test_global_species(self):
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"""Check global species."""
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self.assertEqual(
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self.records["globalSpecies"][0].annotations["organism"], "Mus musculus"
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)
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self.assertEqual(
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self.records["globalSpecies"][0].annotations["ncbi_taxid"], "10090"
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)
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self.assertEqual(
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self.records["globalSpecies"][1].annotations["organism"], "Homo sapiens"
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)
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self.assertEqual(
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self.records["globalSpecies"][1].annotations["ncbi_taxid"], "9606"
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)
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def test_local_source_definition(self):
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"""Check local source."""
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self.assertEqual(self.records["protein"][4].annotations["source"], "Uniprot")
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def test_empty_description(self):
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"""Check empty description."""
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self.assertEqual(
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self.records["rna"][4].description,
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SeqRecord(id="", seq=Seq("")).description,
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)
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class TestReadHeader(unittest.TestCase):
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def test_check_dna_header(self):
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"""Check if the header information is parsed."""
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records = SeqIO.parse("SeqXML/dna_example.xml", "seqxml")
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self.assertEqual(records.source, "Ensembl")
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self.assertEqual(records.sourceVersion, "56")
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self.assertEqual(records.seqXMLversion, "0.4")
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def test_check_rna_header(self):
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"""Check if the header information is parsed."""
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records = SeqIO.parse("SeqXML/rna_example.xml", "seqxml")
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self.assertEqual(records.source, "Ensembl")
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self.assertEqual(records.sourceVersion, "56")
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self.assertEqual(records.seqXMLversion, "0.3")
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def test_check_protein_header(self):
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"""Check if the header information is parsed."""
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records = SeqIO.parse("SeqXML/protein_example.xml", "seqxml")
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self.assertEqual(records.source, "Ensembl")
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self.assertEqual(records.sourceVersion, "56")
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self.assertEqual(records.seqXMLversion, "0.4")
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def test_check_global_species_example_header(self):
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"""Check if the header information is parsed."""
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records = SeqIO.parse("SeqXML/global_species_example.xml", "seqxml")
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self.assertEqual(records.speciesName, "Mus musculus")
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self.assertEqual(records.ncbiTaxID, "10090")
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self.assertEqual(records.source, "Ensembl")
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self.assertEqual(records.sourceVersion, "56")
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self.assertEqual(records.seqXMLversion, "0.4")
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class TestReadAndWrite(unittest.TestCase):
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def test_read_write_rna(self):
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"""Read and write RNA."""
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read1_records = list(SeqIO.parse("SeqXML/rna_example.xml", "seqxml"))
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self._write_parse_and_compare(read1_records)
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def test_read_write_dna(self):
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"""Read and write DNA."""
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read1_records = list(SeqIO.parse("SeqXML/dna_example.xml", "seqxml"))
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self._write_parse_and_compare(read1_records)
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def test_read_write_protein(self):
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"""Read and write protein."""
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read1_records = list(SeqIO.parse("SeqXML/protein_example.xml", "seqxml"))
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self._write_parse_and_compare(read1_records)
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def test_read_write_globalSpecies(self):
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"""Read and write global species."""
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read1_records = list(SeqIO.parse("SeqXML/global_species_example.xml", "seqxml"))
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self._write_parse_and_compare(read1_records)
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def _write_parse_and_compare(self, read1_records):
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handle = BytesIO()
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SeqIO.write(read1_records, handle, "seqxml")
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handle.seek(0)
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read2_records = list(SeqIO.parse(handle, "seqxml"))
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self.assertEqual(len(read1_records), len(read2_records))
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for record1, record2 in zip(read1_records, read2_records):
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assert_equal_records(self, record1, record2)
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def test_write_species(self):
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"""Test writing species from annotation tags."""
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record = SeqIO.read("SwissProt/sp016", "swiss")
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self.assertEqual(record.annotations["organism"], "Homo sapiens (Human)")
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self.assertEqual(record.annotations["ncbi_taxid"], ["9606"])
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handle = BytesIO()
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SeqIO.write(record, handle, "seqxml")
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handle.seek(0)
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output = handle.getvalue()
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text = output.decode("UTF-8")
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self.assertIn("Homo sapiens (Human)", text)
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self.assertIn("9606", text)
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if (
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'<species name="Homo sapiens (Human)" ncbiTaxID="9606"></species>'
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not in text
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):
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raise ValueError("Missing expected <species> tag: %r" % text)
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class TestReadCorruptFiles(unittest.TestCase):
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def test_for_errors(self):
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"""Handling of corrupt files."""
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# SeqIO.parse reads the file in blocks until it finds the seqXML
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# element with global information such as the source and sourceVersion.
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# Since one block is likely large enough to cover the first few
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# entries in the file, the ValueError may be raised after we call
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# SeqIO.parse, before we start iterating over the file.
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def f(path):
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records = SeqIO.parse(path, "seqxml")
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for record in records:
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pass
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self.assertRaises(ValueError, f, "SeqXML/corrupt_example1.xml")
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self.assertRaises(ValueError, f, "SeqXML/corrupt_example2.xml")
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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